QOOH radicals are key intermediates in the chain of reactions leading to the autoignition of hydrocarbons and oxygenated organic compounds. They are thought to undergo two main reactions: OH elimination to form a cyclic ether and HO2 elimination to form an alkene. However, theoretical analysis of various substituted hydroperoxyalkyl radicals has found two new pathways: OH transfer and internal H abstraction assisted OH elimination. To determine the importance of these new pathways, their barrier heights for several substituted alkanes were calculated using various quantum chemical theories and compared to those of the well-known pathways. Several cases revealed possible competition with the well-known pathways. Rate coefficients were calculated for propyl systems but further studies will need to complete rate coefficients and branching fractions for all systems analyzed to understand these new reactions’ role in autoignition.
2,4,dimethyloxetane is an important cyclic ether intermediate that is produced from hydroperoxyalkyl (QOOH) radicals in the low-temperature combustion of n-pentane. However, the reaction mechanisms and rates of consumption pathways remain unclear. In the present work, the pressure- and temperature-dependent kinetics of seven cyclic ether peroxy radicals, which stem from 2,4,dimethyloxetane via H-abstraction and O2 addition, were determined. The automated kinetic workflow code, KinBot, was used to model the complexity of the chemistry in a stereochemically resolved manner and solve the resulting master equations from 300–1000 K and from 0.01–100 atm. The main conclusions from the calculations include (i) diastereomeric cyclic ether peroxy radicals show significantly different reactivities, (ii) the stereochemistry of the peroxy radical determines which QOOH isomerization steps are possible, (iii) conventional QOOH decomposition pathways, such as cyclic ether formation and HO2 elimination, compete with ring-opening reactions, which primarily produce OH radicals, the outcome of which is sensitive to stereochemistry. Ring-opening reactions lead to unique products, such as unsaturated, acyclic peroxy radicals, that form direct connections with species present in other chemical kinetics mechanisms through "cross-over" reactions that may complicate the interpretation of experimental results from combustion of n-pentane and, by extension, other alkanes. For example, one cross-over reaction involving 1-hydroperoxy-4-pentanone-2-yl produces 2-(hydroperoxymethyl)-3-butanone-1-yl, which is an iso-pentane-derived ketohydroperoxide (KHP). At atmospheric pressure, the rate of chemical reactions of all seven peroxy radicals compete with that of collisional stabilization, resulting in well-skipping reactions. However, at 100 atm, only one out of seven peroxy radicals undergoes significant well-skipping reactions. Here, the rates produced from the master equation calculations provide the first foundation for the development of detailed sub-mechanisms for cyclic ether intermediates. In addition, analysis of the complex reaction mechanisms of 2,4-dimethyloxetane-derived peroxy radicals provides insights into the effects of stereoisomers on reaction pathways and product yields.
Depleted uranium hexafluoride (UF6), a stockpiled byproduct of the nuclear fuel cycle, reacts readily with atmospheric humidity, but the mechanism is poorly understood. Here we compare several potential initiation steps at a consistent level of theory, generating underlying structures and vibrational modes using hybrid density functional theory (DFT) and computing relative energies of stationary points with double-hybrid (DH) DFT. A benchmark comparison is performed to assess the quality of DH-DFT data using reference energy differences obtained using a complete-basis-limit coupled-cluster (CC) composite method. The associated large-basis CC computations were enabled by a new general-purpose pseudopotential capability implemented as part of this work. Dispersion-corrected parameter-free DH-DFT methods, namely PBE0-DH-D3(BJ) and PBE-QIDH-D3(BJ), provided mean unsigned errors within chemical accuracy (1 kcal mol-1) for a set of barrier heights corresponding to the most energetically favorable initiation steps. The hydrolysis mechanism is found to proceed via intermolecular hydrogen transfer within van der Waals complexes involving UF6, UF5OH, and UOF4, in agreement with previous studies, followed by the formation of a previously unappreciated dihydroxide intermediate, UF4(OH)2. The dihydroxide is predicted to form under both kinetic and thermodynamic control, and, unlike the alternate pathway leading to the UO2F2 monomer, its reaction energy is exothermic, in agreement with observation. Finally, harmonic and anharmonic vibrational simulations are performed to reinterpret literature infrared spectroscopy in light of this newly identified species.
We present a new geodesic-based method for geometry optimization in a basis set of redundant internal coordinates. Our method updates the molecular geometry by following the geodesic generated by a displacement vector on the internal coordinate manifold, which dramatically reduces the number of steps required to converge to a minimum. Our method can be implemented in any existing optimization code, requiring only implementation of derivatives of the Wilson B-matrix and the ability to numerically solve an ordinary differential equation.
We present a combined experimental and theoretical investigation of the autoignition chemistry of a prototypical cyclic hydrocarbon, cyclopentane. Experiments using a high-pressure photolysis reactor coupled to time-resolved synchrotron VUV photoionization mass spectrometry directly probe the short-lived radical intermediates and products in cyclopentane oxidation reactions. We detect key peroxy radical intermediates ROO and OOQOOH, as well as several hydroperoxides, formed by second O2 addition. Automated quantum chemical calculations map out the R + O2 + O2 reaction channels and demonstrate that the detected intermediates belong to the dominant radical chain-branching pathway: ROO (+ O2) → γ-QOOH + O2 → γ-OOQOOH → products. ROO, OOQOOH, and hydroperoxide products of second-O2 addition undergo extensive dissociative ionization, making their experimental assignment challenging. We use photoionization dynamics calculations to aid in their characterization and report the absolute photoionization spectra of isomerically pure ROO and γ-OOQOOH. A global statistical fit of the observed kinetics enables reliable quantification of the time-resolved concentrations of these elusive, yet critical species, paving the way for detailed comparisons with theoretical predictions from master-equation-based models.
We have extended the computational singular perturbation (CSP) method to differential algebraic equation (DAE) systems and demonstrated its application in a heterogeneous-catalysis problem. The extended method obtains the CSP basis vectors for DAEs from a reduced Jacobian matrix that takes the algebraic constraints into account. We use a canonical problem in heterogeneous catalysis, the transient continuous stirred tank reactor (T-CSTR), for illustration. The T-CSTR problem is modelled fundamentally as an ordinary differential equation (ODE) system, but it can be transformed to a DAE system if one approximates typically fast surface processes using algebraic constraints for the surface species. We demonstrate the application of CSP analysis for both ODE and DAE constructions of a T-CSTR problem, illustrating the dynamical response of the system in each case. We also highlight the utility of the analysis in commenting on the quality of any particular DAE approximation built using the quasi-steady state approximation (QSSA), relative to the ODE reference case.
Chemical kinetics simulations are used to explore whether detailed measurements of relevant chemical species during the oxidation of very dilute fuels (less than 1 Torr partial pressure) in a high-pressure plug flow reactor (PFR) can predict autoignition propensity. We find that for many fuels the timescale for the onset of spontaneous oxidation in dilute fuel/air mixtures in a simple PFR is similar to the 1st-stage ignition delay time (IDT) at stoichiometric engine-relevant conditions. For those fuels that deviate from this simple trend, the deviation is closely related to the peak rate of production of OH, HO2, CH2O, and CO2 formed during oxidation. We use these insights to show that an accurate correlation between simulated profiles of these species in a PFR and 1st-stage IDT can be developed using convolutional neural networks. Our simulations suggest that the accuracy of such a correlation is 10–50%, which is appropriate for rapid fuel screening and may be sufficient for predictive fuel performance modeling.
KinBot is a Python code that automatically characterizes kinetically important stationary points on reactive potential energy surfaces and arranges the results into a form that lends itself easily to master equation calculations. This version of KinBot tackles C, H, O and S atom containing species and unimolecular (isomerization or dissociation) reactions. KinBot iteratively changes the geometry of the reactant to obtain initial guesses for reactive saddle points defined by KinBot's reaction types, which are then optimized by a third-party quantum chemistry package. KinBot verifies the connectivity of the saddle points with the reactant and identifies the products through intrinsic reaction coordinate calculations. New calculations can be automatically spawned from the products to obtain complete potential energy surfaces. The utilities of KinBot include conformer searches, projected frequency and hindered rotor calculations, and the automatic determination of the rotational symmetry numbers. Input files for popular RRKM master equation codes are automatically built, enabling an automated workflow all the way to the calculation of pressure and temperature dependent rate coefficients. Four examples are included. (i) [1,3]-sigmatropic H-migration reactions of unsaturated hydrocarbons and oxygenates are calculated to assess the relative importance of suprafacial and antrafacial reactions. (ii) Saddle points on three products of gamma-valerolactone thermal decomposition are studied and compared to literature potential energy surfaces. (iii) The previously published propene+OH reaction is reproduced to show the capability of building an entire potential energy surface. (iv) All species up to C4 in the Aramco Mech 2.0 are subjected to a KinBot search. Program summary: Program title: KinBot Program files doi: http://dx.doi.org/10.17632/hsh6dvv2zj.1 Licensing provisions: BSD 3-Clause Programming language: Python Supplementary material: 1. A static version of the source code (KinBot.tar), 2. The manual for the static version (KinBot_Manual.pdf) 3. Geometries and energies of the stationary points on the potential energy surface of the sigmatropic reaction search (sigmatropic_H_shift.out) 4. Geometries and energies of the stationary points on the potential energy surface of the propene+ OH central and terminal addition reaction (propene+oh central addition.out, propene+oh terminal addition.out) 5. Geometries and energies of the stationary points on the potential energy surface of gamma valerolactone, 4-pentenoic acid and 3-pentenoic acid (GVL energies and geometries.out, 4PA energies and geometries.out, 3PA energies and geometries.out) 6. Example runs including all input and output files for a one-well search for propanol radical, full PES search for the n-pentyl radical, a search for all homolytic scission in propanol, and the reaction searches for GVL (output.zip) 7. Results of symmetry calculations for a literature benchmark dataset (Symmetry_correct.pdf, Symmetry_wrong.pdf) Nature of problem: Automatic discovery of unimolecular reaction pathways (isomerization and dissociation) for molecules and radicals relevant in gas-phase combustion and atmospheric chemistry, including oxidation and pyrolytic processes for structures including carbon, oxygen, sulfur and hydrogen atoms. The reactants, products, and transition states are characterized using a suite of tools coupled to electronic structure codes, and the results are provided in a format that lends itself easily to calculating rate coefficients based on statistical rate theories with other external codes. Solution method: Reaction pathways are identified using heuristic searches starting from a reactant by iteratively altering its geometry toward a good guess for a transition state for reactions with barriers. The transition state is identified as a first-order saddle point on the potential energy surface, which is located using local optimization methods of third-party quantum chemistry codes. We use intrinsic reaction coordinate calculations to verify the direct connectivity of the saddle point to the reactant and to identify the product species. Conformational searches, hindered rotor potentials, frequency calculations, and high-level optimizations yield the necessary data for RRKM master equation calculations. Additional comments including restrictions and unusual features: KinBot is designed to run on Unix clusters, and is written in Python, compatible with versions 2.7 and 3. It communicates with a PBS or SLURM workload manager to submit quantum chemistry calculations to third-party software. It makes use of a modified fork of ASE for the input writing, calling and output parsing of the quantum chemistry software which has been tested with Gaussian (G09RevD.01). OpenBabel (2.4.1) and RDKit (2018.09.01) are used to convert smiles to internal species representations and for species comparison and results visualization. The output of KinBot can be visualized with the PESViewer script, and graph structures are drawn using NetworkX. The master equation solvers MESS or MESMER are needed to calculate rate coefficients at the end of a given run. This version of KinBot can handle H, C, S, and O atom-containing molecules, and searches for isomerization and dissociation pathways.
Methanol is a benchmark for understanding tropospheric oxidation, but is underpredicted by up to 100% in atmospheric models. Recent work has suggested this discrepancy can be reconciled by the rapid reaction of hydroxyl and methylperoxy radicals with a methanol branching fraction of 30%. However, for fractions below 15%, methanol underprediction is exacerbated. Theoretical investigations of this reaction are challenging because of intersystem crossing between singlet and triplet surfaces – ∼45% of reaction products are obtained via intersystem crossing of a pre-product complex – which demands experimental determinations of product branching. Here we report direct measurements of methanol from this reaction. A branching fraction below 15% is established, consequently highlighting a large gap in the understanding of global methanol sources. These results support the recent high-level theoretical work and substantially reduce its uncertainties.